Cyclone V GT Init/Config Issues

We have a custom FPGA board with the Cyclone V GT device. Part number 5CGTFD9EF35.

What Happens:

There is a rare issue that occurs where the device periodically goes through the init and config cycles potentially delaying the boot up time by a significant margin. The "INIT_DONE" and "CONF_DONE" signals from the Altera are toggling while this is happening. The init/config process restarts very rapidly, multiple times a second. This lasts for several seconds. The init/config completes and stabilizes (the board appears to successfully come up and load its firmware) for a couple seconds and this cycle repeats itself indefinitely.

When it Happens:

The issue is rarely seen from a cold boot, but can be reliably reproduced if the board is power cycled after running for about 45 mins+.

Observations:

During the period where the init/config process is compromised and cycling, we have determined none of the voltages on the board go through any kind of drop. We have also determined that the reset signal going to the altera is not being toggled during this time.

Questions:

What causes the init/config process to lose integrity and start over?

What can we measure to give more insight into the problem?

How can this issue be remedied on future boards?

Thank you.